Virtual Screening for Potential Inhibitors of Human Hexokinase II for the Development of Anti-Dengue Therapeutics

Substantially altered bacterial diversity associated with developmental stages of litchi stink bug, Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae)

The mutualistic symbiotic relationship between insects and bacteria greatly influences the growth and development of host insects. Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae), also referred to as the litchi stink bug, has recently been established as an important insect pest of Litchi chinensis Sonn. and causes substantial yield loss in India. To design effective and environmentally safe management strategies, an understanding of the diversity and functions of microbiota harbored across the development stages is very important. The assessment of the diversity of development-associated bacteria in T. javanica and their predicted functions was conducted using 16S rRNA gene sequences obtained by the Illumina MiSeq technology. The result showed that taxonomic analysis of associated bacteria in different developmental stages includes a total of 46 phyla, encompassing 139 classes, 271 orders, 474 families, and 893 genera of bacteria. All developmental stages of T. javanica shared a total of 42.82 percent of operational taxonomic units (OTUs), with a 97 % similarity threshold. Alpha diversity indices showed maximum species richness in the egg and adult stages. The phyla Proteobacteria followed by Firmicutes, Bacteriodetes, and Actinobacteria, exhibited the highest levels of abundance across all the developmental stages of T. javanica. Microbiota were most different between the egg and the 4th nymphal stage (χ2 = 711.67) and least different between the 2nd and 4th nymphal instars (χ2 = 44.45). The predicted functions of the microbiota associated with T. javanica are mainly involved in amino acid metabolism, cell motility, cellular processes and signaling, glycan biosynthesis and metabolism, lipid metabolism, and membrane transport. The present study documentation and information on symbiotic bacteria across T. javanica life stages will prompt the development of novel biological management strategies.

Multi-GWAS reveals significant genomic regions for Mungbean yellow mosaic India virus resistance in urdbean (Vigna mungo (L.) across multiple environments

KEY MESSAGE

Unraveling genetic markers for MYMIV resistance in urdbean, with 8 high-confidence marker-trait associations identified across diverse environments, provides crucial insights for combating MYMIV disease, informing future breeding strategies. Globally, yellow mosaic disease (YMD) causes significant yield losses, reaching up to 100% in favorable environments within major urdbean cultivating regions. The introgression of genomic regions conferring resistance into urdbean cultivars is crucial for combating YMD, including resistance against mungbean yellow mosaic India virus (MYMIV). To uncover the genetic basis of MYMIV resistance, we conducted a genome-wide association study (GWAS) using three multi-locus models in 100 diverse urdbean genotypes cultivated across six individual and two combined environments. Leveraging 4538 high-quality single nucleotide polymorphism (SNP) markers, we identified 28 unique significant marker-trait associations (MTAs) for MYMIV resistance, with 8 MTAs considered of high confidence due to detection across multiple GWAS models and/or environments. Notably, 4 out of 28 MTAs were found in proximity to previously reported genomic regions associated with MYMIV resistance in urdbean and mungbean, strengthening our findings and indicating consistent genomic regions for MYMIV resistance. Among the eight highly significant MTAs, one localized on chromosome 6 adjacent to previously identified quantitative trait loci for MYMIV resistance, while the remaining seven were novel. These MTAs contain several genes implicated in disease resistance, including four common ones consistently found across all eight MTAs: receptor-like serine-threonine kinases, E3 ubiquitin-protein ligase, pentatricopeptide repeat, and ankyrin repeats. Previous studies have linked these genes to defense against viral infections across different crops, suggesting their potential for further basic research involving cloning and utilization in breeding programs. This study represents the first GWAS investigation aimed at identifying resistance against MYMIV in urdbean germplasm.

Conjugates of 3,5-Bis(arylidene)-4-piperidone and Sesquiterpene Lactones Have an Antitumor Effect via Resetting the Metabolic Phenotype of Cancer Cells

In recent years, researchers have often encountered the significance of the aberrant metabolism of tumor cells in the pathogenesis of malignant neoplasms. This phenomenon, known as the Warburg effect, provides a number of advantages in the survival of neoplastic cells, and its application is considered a potential strategy in the search for antitumor agents. With the aim of developing a promising platform for designing antitumor therapeutics, we synthesized a library of conjugates of 3,5-bis(arylidene)-4-piperidone and sesquiterpene lactones. To gain insight into the determinants of the biological activity of the prepared compounds, we showed that the conjugates of 3,5-bis(arylidene)-4-piperidone and sesquiterpene lactones, which are cytotoxic agents, demonstrate selective activity toward a number of tumor cell lines with glycolysis-inhibiting ability. Moreover, the results of molecular and in silico screening allowed us to identify these compounds as potential inhibitors of the pyruvate kinase M2 oncoprotein, which is the rate-determining enzyme of glycolysis. Thus, the results of our work indicate that the synthesized conjugates of 3,5-bis(arylidene)-4-piperidone and sesquiterpene lactones can be considered a promising platform for designing selective cytotoxic agents against the glycolysis process, which opens new possibilities for researchers involved in the search for antitumor therapeutics among compounds containing piperidone platforms.

Molecular strategies to enhance the keratinase gene expression and its potential implications in poultry feed industry

The tons of keratin waste are produced by the poultry and meat industry which is an insoluble and protein-rich material found in hair, feathers, wool, and some epidermal wastes. These waste products could be degraded and recycled to recover protein, which can save our environment. One of the potential strategy to achieve this target is use of microbial biotreatment which is more convenient, cost-effective, and environment-friendly by formulating hydrolysate complexes that could be administered as protein supplements, bioactive peptides, or animal feed ingredients. Keratin degradation shows great promise for long-term protein and amino acid recycling. According to the MEROPS database, known keratinolytic enzymes currently belong to at least 14 different protease families, including S1, S8, S9, S10, S16, M3, M4, M14, M16, M28, M32, M36, M38, and M55. In addition to exogenous attack (proteases from families S9, S10, M14, M28, M38, and M55), the various keratinolytic enzymes also function via endo-attack (proteases from families S1, S8, S16, M4, M16, and M36). Biotechnological methods have shown great promise for enhancing keratinase expression in different strains of microbes and different protein engineering techniques in genetically modified microbes such as bacteria and some fungi to enhance keratinase production and activity. Some microbes produce specific keratinolytic enzymes that can effectively degrade keratin substrates. Keratinases have been successfully used in the leather, textile, and pharmaceutical industries. However, the production and efficiency of existing enzymes need to be optimized before they can be used more widely in other processes, such as the cost-effective pretreatment of chicken waste. These can be improved more effectively by using various biotechnological applications which could serve as the best and novel approach for recycling and degrading biomass. This paper provides practical insights about molecular strategies to enhance keratinase expression to effectively utilize various poultry wastes like feathers and feed ingredients like soybean pulp. Furthermore, it describes the future implications of engineered keratinases for environment friendly utilization of wastes and crop byproducts for their better use in the poultry feed industry.

Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens

North American salamanders are threatened by intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen Batrachochytrium salamandrivorans (Bsal). To predict potential dispersal of Bsal spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, Bsal, and an introduced but endemic pathogen, B. dendrobatidis (Bd). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and full-length 16S rRNA sequencing. We found that soil microcosms with intact bacterial communities inhibited both Bsal and Bd growth, but inhibitory capacity diminished with increased propagule pressure. Bsal showed greater persistence than Bd. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on properties of their local microbial communities.

Thymus algeriensis Boiss. et Reut., a north African endemic plant species: genetic diversity and population structure as assessed by molecular markers, a pioneer step for conservation implications

BACKGROUND

Thymus algeriensis Boiss. et Reut. is one of the most widespread North African species of the genus Thymus L. The species is subshrub growing primarily in subtropical biome of Morocco, Algeria, Tunisia and Libya. In Tunisia, the plant species is under high pressure of anthropogenic activities including over-collecting. The assessment of genetic diversity and population structure of T. algeriensis is a pioneer step to retrace its evolutionary history and to perform appropriate conservation strategies of the plant species.

METHODS AND RESULTS

Seven wild populations growing, widely, in different bioclimatic zones were selected and analysed using two molecular markers systems. Fifteen Simple Sequence Repeats (SSRs) and fifteen Inter-Simple Sequence Repeats (ISSRs) were used to characterize genetically 140 different genotypes. The results showed a high molecular variation within populations and among the studied genotypes. The intra-populations genetic diversity revealed by SSRs was higher (P = 80.95%, Na = 2.143 and He = 0.364) than that based on ISSRs (P = 78.12%, Na = 1.632, He = 0.265 and I = 0.398). As demonstrated by inbreeding coefficients, a significant level of differentiation and a low level of gene flow were detected among studied populations (FST = 0.161 for SSRs and ΦST = 0.197 for ISSRs). Furthermore, the results of ISSRs marker suggest land strips as barriers in population genetic structure. While SSRs marker reflects a relatively structured bioclimatic patterns of studied populations. The Bayesian analysis showed a specific adaptation of populations to local environments.

CONCLUSIONS

The used molecular markers (ISSRs and SSRs) seem to be effective in deciphering genetic polymorphism of Tunisian genotypes of T. algeriensis. Therefore, the genetic structure of the studied genotypes could constitute a starting point for further conservation, characterization and breeding programs.

Molecular authentication, metabolite profiling and in silico-in vitro cytotoxicity screening of endophytic Penicillium ramusculum from Withania somnifera for breast cancer therapeutics

In the present study, we isolated a potent endophytic fungus from the roots of Withania somnifera. The endophytic fungal strain was authenticated as Penicillium ramusculum SVWS3 based on morphological and molecular sequencing using four gene data and phylogenetic analyses. In vitro cytotoxicity studies unveiled the remarkable cytotoxic potential of the crude extract derived from P. ramusculum, exhibiting dose-dependent effects on MDA-MB-468 and MCF-7 cells. At a concentration of 100 µg/mL, the crude extract resulted in cell viability of 29.78% for MDA-MB-468 cells and 14.61% for MCF-7 cells. The IC50 values were calculated as 62.83 ± 0.93 µg/mL and 17.23 ± 1.43 µg/mL, respectively for MDA-MB-468 and MCF-7 cells. Caspase activation assay established the underlying mechanism of the crude extract depicting the activation of caspases 3 and 7, indicating the induction of apoptosis in MCF-7 cells. Chemotaxonomic profiling elucidated the ability of P. ramusculum to synthesize a diverse array of bioactive compounds, including Fasoracetam, Tryprostatin B, Odorinol, Thyronine, Brevianamide F, Proglumide, Perlolyrine, Tyrphostin B48, Baptifoline, etc. Molecular docking studies inferred that Baptifoline, Brevianamide F, Odorinol, Perlolyrine, Thyronine, Tryphostin B48, and Tryprostatin B were the lead compounds that could effectively interact with the five selected target receptors of breast cancer, further surpassing the positive controls analyzed. Pharmacokinetic profiling revealed that Baptifoline, Odorinol, and Thyronine depicted an excellent therapeutic profile of druggability. These findings collectively substantiate the anticancer activity of bioactive metabolites synthesized by P. ramusculum SVWS3. Hence, the endophytic P. ramusculum SVWS3 can be an authentic source for developing novel chemotherapeutic drug formulations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03906-3.

Synthesis and Primary Activity Assay of Novel Benitrobenrazide and Benserazide Derivatives

Schiff bases attract research interest due to their applications in chemical synthesis and medicinal chemistry. In recent years, benitrobenrazide and benserazide containing imine moiety have been synthesized and characterized as promising inhibitors of hexokinase 2 (HK2), an enzyme overexpressed in most cancer cells. Benserazide and benitrobenrazide possess a common structural fragment, a 2,3,4-trihydroxybenzaldehyde moiety connected through a hydrazone or hydrazine linker acylated on an N' nitrogen atom by serine or a 4-nitrobenzoic acid fragment. To avoid the presence of a toxicophoric nitro group in the benitrobenrazide molecule, we introduced common pharmacophores such as 4-fluorophenyl or 4-aminophenyl substituents. Modification of benserazide requires the introduction of other endogenous amino acids instead of serine. Herein, we report the synthesis of benitrobenrazide and benserazide analogues and preliminary results of inhibitory activity against HK2 evoked by these structural changes. The derivatives contain a fluorine atom or amino group instead of a nitro group in BNB and exhibit the most potent inhibitory effects against HK2 at a concentration of 1 µM, with HK2 inhibition rates of 60% and 54%, respectively.

Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean (Vigna radiata L. Wilczek) using genotyping by sequencing approach

Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r2 = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties.

Chitosan coating silver nanoparticles as a promising feed additive in broilers chicken

The present study aimed to evaluate the potential of chitosan coating silver nanoparticles to enhance the growth performance and immune status of broilers without inducing oxidative stress-related pathological lesions in any organs or leaving residues of silver in the edible parts. Five clusters of Cobb one-day-old chicks (n = 10/group in each replication) were given oral therapy, once a week for 36 days as follows: (1) distilled water, (2, 3) 0.5- and 5 ppm silver nanoparticles (AgNPs), respectively, (4, 5) 0.5- and 5 ppm chitosan/silver nanoconjugates (CS/Ag-NCs), respectively. The results demonstrated a marked elevation in the body weight gain with a decline in the food conversion ratio and marked improvement in feeding and drinking behavior of all nanoparticles treated groups, but higher in CS/Ag-NCs groups than AgNPs groups and control group. In contrast to the 0.5 ppm AgNPs receiving group, the group receiving 5 ppm AgNPs noticed remarkable histological changes in some organs, including the liver, kidneys, spleen, and heart. Moreover, the administration of CS/Ag-NCs at two dosage levels didn't influence any histological changes. The AgNPs groups' antibody titers against the ND and AI viruses were almost identical to those of the control group. Otherwise, CS/Ag-NCs groups recorded the highest antibody titers. Additionally, there was a significant increase in silver content in most edible organs of AgNPs groups at a dosage level of 5 ppm. Otherwise, the coating of AgNPs by CSNPs could decrease the aggregation of silver in the biological organs. Thus, we recommend utilizing 0.5 ppm CS/Ag-NCs in broiler farms to promote their growth performance and strengthen their immune defense.

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet's whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet's whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding

The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.

Diabetic wound healing of aloe vera major phytoconstituents through TGF-β1 suppression via in-silico docking, molecular dynamic simulation and pharmacokinetic studies

To restore the integrity of the skin and subcutaneous tissue, the wound healing process involves a complex series of well-orchestrated biochemical and cellular events. Due to the existence of various active components, accessibility and few side effects, some plant extracts and their phytoconstituents are recognised as viable options for wound healing agents. To find possible inhibitors of diabetic wound healing, four main constituents of aloe vera were identified from the literature. TGF-β1 and the compounds were studied using molecular docking to see how they interacted with the active site of target protein (PDB ID: 6B8Y). The pharmacokinetics investigation of the aloe emodin with the highest dock score complied with all the Lipinski's rule of five and pharmacokinetics criteria. Conformational change in the docked complex of Aloe emodin was investigated with the Amber simulation software, via a molecular dynamic (MD) simulation. The MD simulations of aloe emodin bound to TGF-β1 showed the significant structural rotations and twists occurring from 0 to 200 ns. The estimate of the aloe emodin-TGF-β1 complex's binding free energy has also been done using MM-PBSA/GBSA techniques. Additionally, aloe emodin has a wide range of enzymatic activities since their probability active (Pa) values is >0.700. 'Aloe emodin', an active extract of aloe vera, has been identified as the key chemical in the current investigation that can inhibit diabetic wound healing. Both in-vitro and in-vivo experiments will be used in a wet lab to confirm the current computational findings.Communicated by Ramaswamy H. Sarma.

Repurposing Drugs for Inhibition against ALDH2 via a 2D/3D Ligand-Based Similarity Search and Molecular Simulation

Aldehyde dehydrogenase-2 (ALDH2) is a crucial enzyme participating in intracellular aldehyde metabolism and is acknowledged as a potential therapeutic target for the treatment of alcohol use disorder and other addictive behaviors. Using previously reported ALDH2 inhibitors of Daidzin, CVT-10216, and CHEMBL114083 as reference molecules, here we perform a ligand-based virtual screening of world-approved drugs via 2D/3D similarity search methods, followed by the assessments of molecular docking, toxicity prediction, molecular simulation, and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis. The 2D molecular fingerprinting of ECFP4 and FCFP4 and 3D molecule-shape-based USRCAT methods show good performances in selecting compounds with a strong binding behavior with ALDH2. Three compounds of Zeaxanthin (q = 0), Troglitazone (q = 0), and Sequinavir (q = +1 e) are singled out as potential inhibitors; Zeaxanthin can only be hit via USRCAT. These drugs displayed a stronger binding strength compared to the reported potent inhibitor CVT-10216. Sarizotan (q = +1 e) and Netarsudil (q = 0/+1 e) displayed a strong binding strength with ALDH2 as well, whereas they displayed a shallow penetration into the substrate-binding tunnel of ALDH2 and could not fully occupy it. This likely left a space for substrate binding, and thus they were not ideal inhibitors. The MM-PBSA results indicate that the selected negatively charged compounds from the similarity search and Vina scoring are thermodynamically unfavorable, mainly due to electrostatic repulsion with the receptor (q = -6 e for ALDH2). The electrostatic attraction with positively charged compounds, however, yielded very strong binding results with ALDH2. These findings reveal a deficiency in the modeling of electrostatic interactions (in particular, between charged moieties) in the virtual screening via the 2D/3D similarity search and molecular docking with the Vina scoring system.

Computer-aided anti-cancer drug discovery of EGFR protein based on virtual screening of drug bank, ADMET, docking, DFT and molecular dynamic simulation studies

Numerous malignancies, including breast cancer, non-small cell lung cancer, and chronic myeloid leukemia, are brought on by aberrant tyrosine kinase signaling. Since the current chemotherapeutic medicines are toxic, there is a great need and demand from cancer patients to find novel chemicals that are toxic-free or have low toxicity and that can kill tumor cells and stop their growth. This work describes the in-silico examination of substances from the drug bank as EGFR inhibitors. Firstly, drug-bank was screened using the pharmacophore technique to select the ligands and Erlotinib (DB00530) was used as matrix compound. The selected ligands were screened using ADMET and the hit compounds were subjected to docking. The lead compound from the docking was subjected to DFT and MD simulation study. Using the pharmacophore technique, 23 compounds were found through virtual drug bank screening. One hit molecule from the ADMET prediction was the subject of docking study. According to the findings, DB03365 molecule fits to the EGFR active site by several hydrogen bonding interactions with amino acids. Furthermore, DFT analysis revealed high reactivity for DB03365 compound in the binding pocket of the target protein, based on ELUMO, EHOMO and band energy gap. Furthermore, MD simulations for 100 ns revealed that the ligand interactions with the residues of EGFR protein were part of the essential residues for structural stability and functionality. However, DB03365 was a promising lead molecule that outperformed the reference compound in terms of performance and in-vitro and in-vivo experiments needs to validate the study.Communicated by Ramaswamy H. Sarma.

Physicochemical and functional properties of seed flours obtained from germinated and non-germinated Canavalia gladiata and Mucuna pruriens

C. gladiata and M. pruriens are underutilized legumes available in Sri Lanka. The physicochemical and functional properties of germinated and non-germinated flours from these two legumes were investigated. Protein contents of the flours of C. gladiata and M. pruriens increased by 17.04% and 14.69% respectively while fat and carbohydrate contents decreased due to germination. Higher Fe, Cu, Zn, Mn, and Se content was observed in both germinated flour types. Glutamic acid is the highest non-essential amino acid whereas leucine is the highest essential amino acid found in both flour types. The majority of amino acids in 100 g of seed flour of both legumes increased due to germination. Moreover, some of the functional properties of legume flours were changed such as swelling power, water and oil holding capacities because of the germination. In conclusion, the functional and nutritional properties of flour can be altered by the germination process making them ideal for utilization as ingredients for functional food formulations.

Long-Term Monitoring of Aphid-Transmitted Viruses in Melon and Zucchini Crops: Genetic Diversity and Population Structure of Cucurbit Aphid-Borne Yellows Virus and Watermelon Mosaic Virus

Understanding the emergence and prevalence of viral diseases in crops requires the systematic epidemiological monitoring of viruses, as well as the analysis of how ecological and evolutionary processes combine to shape viral population dynamics. Here, we extensively monitored the occurrence of six aphid-transmitted viruses in melon and zucchini crops in Spain for 10 consecutive cropping seasons between 2011 and 2020. The most prevalent viruses were cucurbit aphid-borne yellows virus (CABYV) and watermelon mosaic virus (WMV), found in 31 and 26% of samples with yellowing and mosaic symptoms. Other viruses, such as zucchini yellow mosaic virus, cucumber mosaic virus, Moroccan watermelon mosaic virus, and papaya ring spot virus, were detected less frequently (<3%) and mostly in mixed infections. Notably, our statistical analysis showed a significant association between CABYV and WMV in melon and zucchini hosts, suggesting that mixed infections might be influencing the evolutionary epidemiology of these viral diseases. We then carried out a comprehensive genetic characterization of the full-length genome sequences from CABYV and WMV isolates by using the Pacific Biosciences single-molecule real-time (PacBio) high-throughput technology to assess the genetic variation and structure of their populations. Our results showed that the CABYV population displayed seven codons under positive selection, and although most isolates clustered in the Mediterranean clade, a subsequent analysis of molecular variance revealed a significant, fine-scale temporal structure, which was in part explained by the level of the variance between isolates from single and mixed infections. In contrast, the WMV population genetic analysis showed that most of the isolates grouped into the Emergent clade, with no genetic differentiation and under purifying selection. These results underlie the epidemiological relevance of mixed infections for CABYV and provide a link between genetic diversity and CABYV dynamics at the whole-genome level.

Association between tumor necrosis factor-alpha polymorphisms (rs361525, rs1800629, rs1799724, 1800630, and rs1799964) and risk of psoriasis in studies following Hardy-Weinberg equilibrium: A systematic review and meta-analysis

Objective

Psoriasis is a disease with an immunogenetic background in which cytokines have important effects on its prevalence and incidence. The present meta-analysis evaluated the relationship between tumor necrosis factor-alpha (TNF-α) polymorphisms (rs361525, rs1800629, rs1799724, 1800630, and rs1799964) and psoriasis risk in studies following Hardy-Weinberg equilibrium (HWE).

Materials and methods

Four databases were searched to retrieve relevant studies reporting the distributions of TNF-α polymorphisms in psoriasis cases compared to controls. The effect sizes were the 95% confidence intervals (CIs) and odds ratios (ORs). Subgroup analysis, sensitivity analyses, publication bias, trial sequential analysis (TSA), and meta-regression were performed on the initial pooled results of TNF-α polymorphisms.

Results

Thirty-six articles with 71 studies were included in the meta-analysis (twenty-six: rs361525, twenty-seven: rs1800629, nine: rs1799724, four: 1800630, and five: rs1799964). The pooled ORs for -238 G/A rs361525 polymorphism were 2.33 (p < 0.00001), 2.79 (p < 0.0001), 2.35 (p < 0.00001), 2.44 (p < 0.00001), and 2.45 (p < 0.00001), as well as 1.57 (p < 0.00001), 1.98 (p = 0.01), 1.61 (p < 0.00001), 1.64 (p < 0.00001), and 1.79 (p < 0.00001) for -857 C/T rs1799724 polymorphism in allelic, homozygous, heterozygous, dominant, and recessive models, respectively. Ethnicity, psoriasis type, and sample size affected the pooled results of rs361525, rs1800629, and rs1799724 polymorphisms. Based on TSA, there were just sufficient cases for -238 G/A rs361525 polymorphism in five genetic models and -857C/T rs1799724 polymorphism in allelic, heterozygous, and dominant models.

Conclusions

The A allele and GA and GG genotypes of -238 G/A rs361525 polymorphism and T allele, TT and CT genotypes of -857C/T rs1799724 polymorphism were related to increased risks in psoriasis cases. Well-designed studies (with no deviation from HWE in controls) with more cases are recommended in the future.

Design and Identification of a Novel Antiviral Affinity Peptide against Fowl Adenovirus Serotype 4 (FAdV-4) by Targeting Fiber2 Protein

Outbreaks of hydropericardium hepatitis syndrome caused by fowl adenovirus serotype 4 (FAdV-4) with a novel genotype have been reported in China since 2015, with significant economic losses to the poultry industry. Fiber2 is one of the important structural proteins on FAdV-4 virions. In this study, the C-terminal knob domain of the FAdV-4 Fiber2 protein was expressed and purified, and its trimer structure (PDB ID: 7W83) was determined for the first time. A series of affinity peptides targeting the knob domain of the Fiber2 protein were designed and synthesized on the basis of the crystal structure using computer virtual screening technology. A total of eight peptides were screened using an immunoperoxidase monolayer assay and RT-qPCR, and they exhibited strong binding affinities to the knob domain of the FAdV-4 Fiber2 protein in a surface plasmon resonance assay. Treatment with peptide number 15 (P15; WWHEKE) at different concentrations (10, 25, and 50 μM) significantly reduced the expression level of the Fiber2 protein and the viral titer during FAdV-4 infection. P15 was found to be an optimal peptide with antiviral activity against FAdV-4 in vitro with no cytotoxic effect on LMH cells up to 200 μM. This study led to the identification of a class of affinity peptides designed using computer virtual screening technology that targeted the knob domain of the FAdV-4 Fiber2 protein and may be developed as a novel potential and effective antiviral strategy in the prevention and control of FAdV-4.

Methyl jasmonate and salicylic acid as powerful elicitors for enhancing the production of secondary metabolites in medicinal plants: an updated review

Plant secondary metabolites are bioactive scaffolds that are crucial for plant survival in the environment and to maintain a defense mechanism from predators. These compounds are generally present in plants at a minimal level and interestingly, they are found to have a wide variety of therapeutic values for humans. Several medicinal plants are used for pharmaceutical purposes due to their affordability, fewer adverse effects, and vital role in traditional remedies. Owing to this reason, these plants are exploited at a high range worldwide and therefore many medicinal plants are on the threatened list. There is a need of the hour to tackle this major problem, one effective approach called elicitation can be used to enhance the level of existing and novel plant bioactive compounds using different types of elicitors namely biotic and abiotic. This process can be generally achieved by in vitro and in vivo experiments. The current comprehensive review provides an overview of biotic and abiotic elicitation strategies used in medicinal plants, as well as their effects on secondary metabolites enhancement. Further, this review mainly deals with the enhancement of biomass and biosynthesis of different bioactive compounds by methyl jasmonate (MeJA) and salicylic acid (SA) as elicitors of wide medicinal plants in in vitro by using different cultures. The present review was suggested as a significant groundwork for peers working with medicinal plants by applying elicitation strategies along with advanced biotechnological approaches.

Occurrence and transport of SARS-CoV-2 in wastewater streams and its detection and remediation by chemical-biological methods

This paper explains the transmission of SARS-CoV and influences of several environmental factors in the transmission process. The article highlighted several methods of collection, sampling and monitoring/estimation as well as surveillance tool for detecting SARS-CoV in wastewater streams. In this context, WBE (Wastewater based epidemiology) is found to be the most effective surveillance tool. Several methods of genomic sequencing are discussed in the paper, which are applied in WBE, like qPCR-based wastewater testing, metagenomics-based analysis, next generation sequencing etc. Additionally, several types of biosensors (colorimetric biosensor, mobile phone-based biosensors, and nanomaterials-based biosensors) showed promising results in sensing SARS-CoV in wastewater. Further, this review paper outlined the gaps in assessing the factors responsible for transmission and challenges in detection and monitoring along with the remediation and disinfection methods of this virus in wastewater. Various methods of disinfection of SARS-CoV-2 in wastewater are discussed (primary, secondary, and tertiary phases) and it is found that a suite of disinfection methods can be used for complete disinfection/removal of the virus. Application of ultraviolet light, ozone and chlorine-based disinfectants are also discussed in the context of treatment methods. This study calls for continuous efforts to gather more information about the virus through continuous monitoring and analyses and to address the existing gaps and identification of the most effective tool/ strategy to prevent SARS-CoV-2 transmission. Wastewater surveillance can be very useful in effective surveillance of future pandemics and epidemics caused by viruses, especially after development of new technologies in detecting and disinfecting viral pathogens more effectively.

Biogenic synthesis of gold nanoparticles using Satureja rechingeri Jamzad: a potential anticancer agent against cisplatin-resistant A2780CP ovarian cancer cells

Drug resistance of cancer cells is a major issue in cancer treatment. Plant-mediated nanoparticle synthesis has been applied in recent years to overcome this problem. In this study, the biogenic synthesis of AuNPs was explored using Satureja rechingeri Jamzad aqueous leaf extract, and their anticancer effects were evaluated in cisplatin-resistant A2780CP ovarian cancer cells. The chemical composition of S. rechingeri Jamzad was analyzed using gas chromatography-mass spectrometry. The characteristics of green-synthesized AuNPs were confirmed using XRD, FTIR, UV-visible spectroscopy, TEM, SEM, EDX, DLS, and zeta potential. The cytotoxic effects of AuNPs and S. rechingeri Jamzad aqueous extract on cisplatin-resistant A2780CP ovarian cancer cells were evaluated by MTT assay and flow cytometry. Real-time PCR analyzed gene expression. The chemical composition revealed that carvacrol (89%) was the main component of the S. rechingeri Jamzad extract. The average size of the spherical biosynthesized AuNPs was 15.1 ± 3.7 nm. The AuNPs and plant extract inhibited the growth of cisplatin-resistant ovarian cancer cells in a time- and dose-dependent manner. The apoptotic cell death was confirmed by flow cytometry and DAPI staining. The proapoptotic genes were upregulated, while anti-apoptotic and metastatic genes were downregulated. According to the cell cycle analysis, cancer cells were arrested in the G0/G1 phase. Considering the anticancer activity of the synthesized AuNPs using S. rechingeri Jamzad and the low side effects of AuNPs on normal cells, these AuNPs showed strong potential for use as biological agents in drug-resistant cancer cells treatment.

Pharmacophore-based virtual screening and in-silico study of natural products as potential DENV-2 RdRp inhibitors

Dengue fever is a significant public health concern throughout the world, causing an estimated 500,000 hospitalizations and 20,000 deaths each year, despite the lack of effective therapies. The DENV-2 RdRp has been identified as a potential target for the development of new and effective dengue therapies. This research's primary objective was to discover an anti-DENV inhibitor using in silico ligand- and structure-based approaches. To begin, a ligand-based pharmacophore model was developed, and 130 distinct natural products (NPs) were screened. Docking of the pharmacophore-matched compounds were performed to the active site of DENV-2 RdRp protease . Eleven compounds were identified as potential DENV-2 RdRp inhibitors based on docking energy and binding interactions. ADMET and drug-likeness were done to predict their pharmacologic, pharmacokinetic, and drug-likeproperties . Compounds ranked highest in terms of pharmacokinetics and drug-like appearances were then subjected to additional toxicity testing to determine the leading compound. Additionally, MD simulation of the lead compound was performed to confirm the docked complex's stability and the binding site determined by docking. As a result, the lead compound (compound-108) demonstrated an excellent match to the pharmacophore, a strong binding contact and affinity for the RdRp enzyme, favourable pharmacokinetics, and drug-like characteristics. In summary, the lead compound identified in this study could be a possible DENV-2 RdRp inhibitor that may be further studied on in vitro and in vivo models to develop as a drug candidate.Communicated by Ramaswamy H. Sarma.

3D-QSAR Studies, Molecular Docking, Molecular Dynamic Simulation, and ADMET Proprieties of Novel Pteridinone Derivatives as PLK1 Inhibitors for the Treatment of Prostate Cancer

Overexpression of polo-like kinase 1 (PLK1) has been found in many different types of cancers. With its essential role in cell proliferation, PLK1 has been determined to be a broad-spectrum anti-cancer target. In this study, 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations were applied on a series of novel pteridinone derivatives as PLK1 inhibitors to discover anti-cancer drug candidates. In this work, three models—CoMFA (Q² = 0.67, R² = 0.992), CoMSIA/SHE (Q² = 0.69, R² = 0.974), and CoMSIA/SEAH (Q² = 0.66, R² = 0.975)—of pteridinone derivatives were established. The three models that were established gave Rpred2 = 0.683, Rpred 2= 0.758, and Rpred 2= 0.767, respectively. Thus, the predictive abilities of the three proposed models were successfully evaluated. The relations between the different champs and activities were well-demonstrated by the contour chart of the CoMFA and CoMSIA/SEAH models. The results of molecular docking indicated that residues R136, R57, Y133, L69, L82, and Y139 were the active sites of the PLK1 protein (PDB code: 2RKU), in which the more active ligands can inhibit the enzyme of PLK1. The results of the molecular dynamic MD simulation diagram were obtained to reinforce the previous molecular docking results, which showed that both inhibitors remained stable in the active sites of the PLK1 protein (PDB code: 2RKU) for 50 ns. Finally, a check of the ADME-Tox properties of the two most active molecules showed that molecular N° 28 could represent a good drug candidate for the therapy of prostate cancer diseases.

Purification of an antiviral protein from the seeds of quinoa (Chenopodium quinoa Willd.) and characterization of its antiviral properties

Plant viral pathogens cause damaging diseases in many agriculture systems, and emerging viral infections are a serious threat for providing adequate food to a continuously growing population. Recent studies of biogenic substances have provided new opportunities for producing novel antiviral agents. The present work has been conducted to evaluate the antiviral activity of quinoa (Chenopodium quinoa Willd.) seeds crude extract. The antiviral activity was retained in different buffer solutions of various pH ranges (5.2-8.5) and remained after the diafiltration process. The putative virus inhibitor was sensitive to treatment with sodium dodecyl sulfate and trichloroacetic acid. An antiviral protein with ~ 25 kDa molecular weight was isolated from the seed quinoa extract using ammonium sulfate precipitation, anion and cation exchange chromatography. The purified protein (Quinoin-I) significantly inhibited TMV on tobacco leaves with an IC₅₀ value at a 6.81 μg/ml concentration. Enzyme activity assay revealed the RNase activity of Quinoin-I, and this feature was retained in the presence of β-mercaptoethanol and ethylene diamine tetraacetic acid. This antiviral protein has been shown as a promising leading molecule for further development as a novel antiviral agent.

Supportive effect of naringenin on NaCl-induced toxicity in Carthamus tinctorius seedlings

In the present study, we used exogenous naringenin (0.5 mM) pretreatment before the stress (25 mM NaCl) on the growth and tolerance of safflower seedlings under non-salinity conditions and salinity conditions. Our results showed that salinity treatment significantly declined the biomass, leaf relative water content, chlorophyll content, K⁺ content, and K⁺/Na⁺ ratio by 28%, 28%, 12%, 36%, and 56%, respectively, as compared to untreated control. The results obtained in the present study showed the beneficial effects of the pretreatment of naringenin in safflower seedlings under non-salinity conditions concerning increasing plant biomass, total phenolic compound, radical scavenging activity (RSA), soluble sugar content, proline, glutathione, enzymatic antioxidants, and K⁺ content. Nevertheless, naringenin pretreated plants showed a clear increment in the values of biomass, RSA, total phenolic compound, and catalase enzyme activity parameters under salinity stress. Salinity stress caused ionic phytotoxicity and oxidative stress by enhancing Na⁺ content, H₂O₂ accumulation, malondialdehyde (MDA), and antioxidants. However, naringenin alleviated salt-induced oxidative stress by decreasing H₂O₂ and MDA content in the leaves and improving the catalase activity in treated plants. Generally, it could be concluded pretreatment of naringenin before stress could partly diminish NaCl-caused oxidative stress in safflower seedlings, probably due to improvement in enzymatic and non-enzymatic antioxidants and reduced cell membrane damage.

Nanoparticles Containing Oxaliplatin and the Treatment of Colorectal Cancer

BACKGROUND

Colorectal cancer (CRC) is a highly widespread malignancy and ranks as the second most common cause of cancer-related mortality.

OBJECTIVE

Cancer patients, including those with CRC, who undergo chemotherapy, are often treated with platinum- based anticancer drugs such as oxaliplatin (OXA). Nevertheless, the administration of OXA is associated with a range of gastrointestinal problems, neuropathy, and respiratory tract infections. Hence, it is necessary to devise a potential strategy that can effectively tackle these aforementioned challenges. The use of nanocarriers has shown great potential in cancer treatment due to their ability to minimize side effects, target drugs directly to cancer cells, and improve drug efficacy. Furthermore, numerous studies have been published regarding the therapeutic efficacy of nanoparticles in the management of colorectal cancer.

METHODS

In this review, we present the most relevant nanostructures used for OXA encapsulation in recent years, such as solid lipid nanoparticles, liposomes, polysaccharides, proteins, silica nanoparticles, metal nanoparticles, and synthetic polymer-carriers. Additionally, the paper provides a summary of the disadvantages and limits associated with nanoparticles.

RESULTS

The use of different carriers for the delivery of oxaliplatin increased the efficiency and reduced the side effects of the drug. It has been observed that the majority of research investigations have focused on liposomes and polysaccharides.

CONCLUSION

This potentially auspicious method has the potential to enhance results and enhance the quality of life for cancer patients undergoing chemotherapy. However, additional investigation is required to ascertain the most suitable medium for the transportation of oxaliplatin and to assess its efficacy through clinical trials.

Fitness dependent optimizer with neural networks for COVID-19 patients

The Coronavirus, known as COVID-19, which appeared in 2019 in China, has significantly affected the global health and become a huge burden on health institutions all over the world. These effects are continuing today. One strategy for limiting the virus's transmission is to have an early diagnosis of suspected cases and take appropriate measures before the disease spreads further. This work aims to diagnose and show the probability of getting infected by the disease according to textual clinical data. In this work, we used five machine learning techniques (GWO_MLP, GWO_CMLP, MGWO_MLP, FDO_MLP, FDO_CMLP) all of which aim to classify Covid-19 patients into two categories (Positive and Negative). Experiments showed promising results for all used models. The applied methods showed very similar performance, typically in terms of accuracy. However, in each tested dataset, FDO_MLP and FDO_CMLP produced the best results with 100% accuracy. The other models' results varied from one experiment to the other. It is concluded that the models on which the FDO algorithm was used as a learning algorithm had the possibility of obtaining higher accuracy. However, it is found that FDO has the longest runtime compared to the other algorithms. The link to the Covid 19 models is found here: https://github.com/Tarik4Rashid4/covid19models.

An overview on the conversion of glycerol to value-added industrial products via chemical and biochemical routes

Glycerol is a common by-product of industrial biodiesel syntheses. Due to its properties, availability, and versatility, residual glycerol can be used as a raw material in the production of high value-added industrial inputs and outputs. In particular, products like hydrogen, propylene glycol, acrolein, epichlorohydrin, dioxalane and dioxane, glycerol carbonate, n-butanol, citric acid, ethanol, butanol, propionic acid, (mono-, di-, and triacylglycerols), cynamoil esters, glycerol acetate, benzoic acid, and other applications. In this context, the present study presents a critical evaluation of the innovative technologies based on the use of residual glycerol in different industries, including the pharmaceutical, textile, food, cosmetic, and energy sectors. Chemical and biochemical catalysts in the transformation of residual glycerol are explored, along with the factors to be considered regarding the choice of catalyst route used in the conversion process, aiming at improving the production of these industrial products.

Heterologous expression, molecular studies and biochemical characterization of a novel alkaline esterase gene from Bacillus thuringiensis for detergent industry

Present study was aimed to clone and express the esterase encoding gene from Bacillus thuringiensis in E. coli BL21. Purification of recombinant esterase enzyme was achieved up to 48.6 purification folds by ion exchange chromatography with specific activity of 126.36 U mg^-1. Molecular weight of esterase enzyme was 29 kDa as measured by SDS-PAGE. Purified esterase enzyme showed stability up to 90% at 90 °C and remained stable in a wide pH range (8-11). Molecular docking strengthens the experimental results by showing the higher binding energy with p-NP-butyrate. Enzyme activity was found to be reduced by EDTA but enhanced in the presence of other metal ions. Enzyme activity was reduced with 1% SDS, PMSF, and urea but organic solvents did not show considerable impact on it even at higher concentrations. Purified recombinant esterase was also found to be compatible with commercial laundry detergents and showed very good stability (up to 90%). All these properties proved the esterase enzyme from B. thuringensis a significant addition in detergent industry.

Evaluating the Role of Wastewaters as Reservoirs of Antibiotic-Resistant ESKAPEE Bacteria Using Phenotypic and Molecular Methods

Introduction

Methodology

Results

Conclusion

Metal-organic framework MIL-100(Fe) as a promising sensor for COVID-19 biomarkers detection

The development of fast and non-invasive techniques to detect SARS-CoV-2 virus at the early stage of the infection would be highly desirable to control the COVID-19 outbreak. Metal-organic frameworks (MOFs) are porous materials with uniform porous structures and tunable pore surfaces, which would be essential for the selective sensing of the specific COVID-19 biomarkers. However, the use of MOFs materials to detect COVID-19 biomarkers has not been demonstrated so far. In this work, for the first time, we employed the density functional theory calculations to investigate the specific interactions of MOFs and the targeted biomarkers, in which the interactions were confirmed by experiment. The five dominant COVID-19 biomarkers and common exhaled gases are comparatively studied by exposing them to MOFs, namely MIL-100(Al) and MIL-100(Fe). The adsorption mechanism, binding site, adsorption energy, recovery time, charge transfer, sensing response, and electronic structures are systematically investigated. We found that MIL-100(Fe) has a higher sensing performance than MIL-100(Al) in terms of sensitivity and selectivity. MIL-100(Fe) shows sensitive to COVID-19 biomarkers, namely 2-methylpent-2-enal and 2,4-octadiene with high sensing responses as 7.44 x 10⁵ and 9 x 10⁷ which are exceptionally higher than those of the common gases which are less than 6. The calculated recovery times of 0.19 and 1.84 x 10^-4 s are short enough to be a resuable sensor. An experimental study also showed that the MIL-100(Fe) provides a sensitivity toward 2-methylpent-2-enal. In conclusion, we suggest that MIL-100(Fe) could be used as a potential sensor for the exhaled breath analysis. We hope that our research can aid in the development of a biosensor for quick and easy COVID-19 biomarker detection in order to control the current pandemic.

Diversity of endophytic fungal community in Huperzia serrata from different ecological areas and their correlation with Hup A content

Background

Huperzine A (Hup A) has attracted considerable attention as an effective therapeutic candidate drug used to treat Alzheimer’s disease. Whereas, the production of Hup A from wild plants faced a major challenge, which is the wild Huperzia Serrata harbor a low Hup A content, has a long-life cycle, and has a small yield. At present, several reports showed that Hup A is produced by various endophytic fungal strains isolated from H. serrata, thereby providing an alternative method to produce the compound and reduce the consumption of this rare and endangered plant. However, till now, very few comprehensive studies are available on the biological diversity and structural composition of endophytic fungi and the effects of endophytic fungi on the Hup A accumulation in H. serrata.

Results

In this research, the composition and diversity of fungal communities in H. serrata were deciphered based on high-throughput sequencing technology of fungal internal transcribed spacer regions2 (ITS2). The correlation between endophytic fungal community and Hup A content was also investigated. Results revealed that the richness and the diversity of endophytic fungi in H. serrata was various according to different tissues and different ecological areas. The endophytic fungal communities of H. serrata exhibit species-specific, ecological-specific, and tissue-specific characteristics. There are 6 genera (Ascomycota_unclassified, Cyphellophora, Fungi_unclassified, Sporobolomyces, and Trichomeriaceae_unclassified) were significantly positively correlated with Hup A content in all two areas, whereas, there are 6 genera (Auricularia, Cladophialophora, Cryptococcus, Mortierella, and Mycena) were significantly negatively correlated with Hup A content of in all two areas.

Conclusions

This study indicated a different composition and diverse endophytic fungal communities in H. serrata from different organs and ecological areas. The current study will provide the realistic basis and theoretical significance for understanding the biological diversity and structural composition of endophytic fungal communities in H. serrata, as well as providing novel insights into the interaction between endophytic fungi and Hup A content.

Biotechnological interventions and indole alkaloid production in Rauvolfia serpentina

Rauvolfia serpentina (L). Benth. ex Kurz. (Apocynaceae), commonly known as Sarpagandha or Indian snakeroot, has long been used in the traditional treatment of snakebites, hypertension, and mental illness. The plant is known to produce an array of indole alkaloids such as reserpine, ajmaline, amalicine, etc. which show immense pharmacological and biomedical significance. However, owing to its poor seed viability, lesser germination rate and overexploitation for several decades for its commercially important bioactive constituents, the plant has become endangered in its natural habitat. The present review comprehensively encompasses the various biotechnological tools employed in this endangered Ayurvedic plant for its in vitro propagation, role of plant growth regulators and additives in direct and indirect regeneration, somatic embryogenesis and synthetic seed production, secondary metabolite production in vitro, and assessment of clonal fidelity using molecular markers and genetic transformation. In addition, elicitation and other methods of optimization of its indole-alkaloids are also described herewith. KEY POINTS: • Latest literature on in vitro propagation of Rauvolfia serpentina • Biotechnological production and optimization of indole alkaloids • Clonal fidelity and transgenic studies in R. serpentina.

Nanomaterials and metal-organic frameworks for biosensing applications of mutations of the emerging viruses

The world today lives in a state of terrible fear due to the mutation of the emerging COVID-19. With the continuation of this pandemic, there is an urgent need for fast, accurate testing devices to detect the emerging SARS-CoV-2 pandemic in terms of biosensors and point-of-care testing. Besides, the urgent development in personal defense tools, anti-viral surfaces and wearables, and smartphones open the door for simplifying the self-diagnosis process everywhere. This review introduces a quick COVID-19 overview: definition, transmission, pathophysiology, the identification and diagnosis, mutation and transformation, and the global situation. It also focuses on an overview of the rapidly advanced technologies based on nanomaterials and MOFs for biosensing, diagnosing, and viral control of the SARS-CoV-2 pandemic. Finally, highlight the latest technologies, applications, existing achievements, and preventive diagnostic strategies to control this epidemic and combat the emerging coronavirus. This humble effort aims to provide a helpful survey that can be used to develop a creative solution and to lay down the future vision of diagnosis against COVID-19.

Multi-omics reveals mechanisms of resistance to potato root infection by Spongospora subterranea

The pathogen Spongospora subterranea infects potato roots and developing tubers resulting in tuber yield and quality losses. Currently, there are no fully effective treatments for disease control. Host resistance is an important tool in disease management and understanding the molecular mechanisms of defence responses in roots of potato plants is required for the breeding of novel resistant cultivars. Here, we integrated transcriptomic and proteomic datasets to uncover these mechanisms underlying S. subterranea resistance in potato roots. This multi-omics approach identified upregulation of glutathione metabolism at the levels of RNA and protein in the resistant cultivar but not in the susceptible cultivar. Upregulation of the lignin metabolic process, which is an important component of plant defence, was also specific to the resistant cultivar at the transcriptome level. In addition, the inositol phosphate pathway was upregulated in the susceptible cultivar but downregulated in the resistant cultivar in response to S. subterranea infection. We provide large-scale multi-omics data of Spongospora-potato interaction and suggest an important role of glutathione metabolism in disease resistance.

A waste-to-wealth initiative exploiting the potential of Anabaena variabilis for designing an integrated biorefinery

The current research work was an innovative approach providing dual advantages of waste bioremediation and an effective biorefinery. The study attempted to exploit wastewater like aqua discharge and solid wastes like poultry litter/cow dung for cyanobacterial cultivation. Aqua discharge appended with 7.5 g L⁻¹ poultry litter turned out as the best combination generating 46% higher carbohydrate yield than BG-11 control. A. variabilis cultivation in this waste-utilized medium also revealed its excellent bioremediation ability. While 100% removal was observed for nitrite, nitrate, and orthophosphate, a respective 74% and 81% reduction was noted for ammonium and total organic carbon. Chemical and biological oxygen demands were also reduced by 90%. This work was also novel in developing a sequential design for the production of bioethanol and co-products like exopolysaccharides, sodium copper chlorophyllin, C-phycocyanin, and poly-β-hydroxybutyrate from the same cyanobacterial biomass. The developed biorefinery implementing the waste-utilized medium was one of its kind, enabling biomass valorization of 61%. Therefore, the present study would provide a leading-edge for tackling the high production costs that limit the practical viability of biorefinery projects. The recyclability of the bioremediated wastewater would not only curtail freshwater usage, the waste disposal concerns would also be mitigated to a great extent.

Cross-continental admixture in the Kho population from northwest Pakistan

Northern Pakistan is home to many diverse ethnicities and languages. The region acted as a prime corridor for ancient invasions and population migrations between Western Eurasia and South Asia. Kho, one of the major ethnic groups living in this region, resides in the remote and isolated mountainous region in the Chitral Valley of the Hindu Kush Mountain range. They are culturally and linguistically distinct from the rest of the Pakistani population groups and their genetic ancestry is still unknown. In this study, we generated genome-wide genotype data of ~1 M loci (Illumina WeGene array) for 116 unrelated Kho individuals and carried out comprehensive analyses in the context of worldwide extant and ancient anatomically modern human populations across Eurasia. The results inferred that the Kho can trace a large proportion of their ancestry to the population who migrated south from the Southern Siberian steppes during the second millennium BCE ~110 generations ago. An additional wave of gene flow from a population carrying East Asian ancestry was also identified in the Kho that occurred ~60 generations ago and may possibly be linked to the expansion of the Tibetan Empire during 7th to 9th centuries CE (current era) in the northwestern regions of the Indian sub-continent. We identified several candidate regions suggestive of positive selection in the Kho, that included genes mainly involved in pigmentation, immune responses, muscular development, DNA repair, and tumor suppression.

Tumor Suppressor microRNAs in Gastrointestinal Cancers: A Mini-Review

BACKGROUND

Gastrointestinal (GI) cancer is associated with a group of cancers affecting the organs in the GI tract, with a high incidence and mortality rate. This type of cancer development involves a series of molecular events that arise by the dysregulation of gene expressions and microRNAs (miRNAs).

OBJECTIVES

This mini-review focuses on elucidating the mechanism of tumor suppressor miRNA-mediated oncogenic gene silencing, which may contribute to a better understanding of miRNA-mediated gene expression regulation of cell cycle, proliferation, invasion, and apoptosis in GI cancers. In this review, the biological significance of tumor suppressor miRNAs involved in gastrointestinal cancers is briefly explained.

METHODS

The articles were searched with the keywords 'miRNA', 'gastrointestinal cancers', 'esophageal cancer', 'gastric cancer', 'colorectal cancer', 'pancreatic cancer', 'liver cancer', and 'gall bladder cancer' from the Google Scholar and PubMed databases. A total of 71 research and review articles have been collected and referred for this study.

RESULTS

This review summarises recent research enhancing the effectiveness of miRNAs as novel prognostic, diagnostic, and therapeutic markers for GI cancer treatment strategies. The expression pattern of various miRNAs has been dysregulated in GI cancers, which are associated with proliferation, cell cycle regulation, apoptosis, migration, and invasion.

CONCLUSION

The role of tumor suppressor miRNAs in the negative regulation of oncogenic gene expression was thoroughly explained in this review. Its potential role as a microRNA therapeutic candidate is also discussed. Profiling and regulating tumor suppressor miRNA expression in gastrointestinal cancers using miRNA mimics could be used as a prognostic, diagnostic, and therapeutic marker, as well as an elucidating molecular therapeutic approach to tumor suppression.

A tau class GST, OsGSTU5, interacts with VirE2 and modulates the Agrobacterium-mediated transformation in rice

OsGSTU5 interacts and glutathionylates the VirE2 protein of Agrobacterium and its (OsGSTU5) overexpression and downregulation showed a low and high AMT efficiency in rice, respectively. During Agrobacterium-mediated transformation (AMT), T-DNA along with several virulence proteins such as VirD2, VirE2, VirE3, VirD5, and VirF enter the plant cytoplasm. VirE2 serves as a single-stranded DNA binding (SSB) protein that assists the cytoplasmic trafficking of T-DNA inside the host cell. Though the regulatory roles of VirE2 have been established, the cellular reaction of their host, especially in monocots, has not been characterized in detail. This study identified a cellular interactor of VirE2 from the cDNA library of rice. The identified plant protein encoded by the gene cloned from rice was designated OsGSTU5, it interacted specifically with VirE2 in the host cytoplasm. OsGSTU5 was upregulated during Agrobacterium infection and involved in the post-translational glutathionylation of VirE2 (gVirE2). Interestingly, the in silico analysis showed that the 'gVirE2 + ssDNA' complex was structurally less stable than the 'VirE2 + ssDNA' complex. The gel shift assay also confirmed the attenuated SSB property of gVirE2 over VirE2. Moreover, knock-down and overexpression of OsGSTU5 in rice showed increased and decreased T-DNA expression, respectively after Agrobacterium infection. The present finding establishes the role of OsGSTU5 as an important target for modulation of AMT efficiency in rice.

Recent trends and advances in polyindole-based nanocomposites as potential antimicrobial agents: a mini review

Infections caused by multi-drug resistant microbes are a big challenge to the medical field and it necessitates the need for new biomedical agents that can act as potential candidates against these pathogens. Several polyindole based nanocomposites were found to exhibit the ability to release reactive oxygen species (ROS) and hence they show excellent antimicrobial properties. The features of polyindole can be fine-tuned to make them potential alternatives to antibiotics and antifungal medicines. This review clearly portrays the antimicrobial properties of polyindole based nanocomposites, reported so far for biomedical applications. This review will give a clear insight into the scope and possibilities for further research on the biomedical applications of polyindole based nanocomposites.

Chemical Advances in Therapeutic Application of Exosomes and Liposomes

Exosomes and liposomes are vesicular nanoparticles that can encapsulate functional cargo. The chemical similarities between naturally occurring exosomes and synthetic liposomes have accelerated the development of exosome mimetics as a therapeutic drug delivery platform under physiological and pathological environments. To maximise the applications of exosomes and liposomes in the clinical setting, it is essential to look into their basic chemical properties and utilise these characteristics to optimise the preparation, loading, modification and hybridisation. This review summarises the chemical and biological properties of both exosomal and liposomal systems as well as some of the challenges related to their production and application. This article concludes with a discussion on potential perspectives for the integration of exosomal and liposomal technologies in mapping better approaches for their biomedical use, especially in therapeutics.

Green approaches for the synthesis of metal and metal oxide nanoparticles using microbial and plant extracts

Green synthesis approaches are gaining significance as promising routes for the sustainable preparation of nanoparticles, offering reduced toxicity towards living organisms and the environment. Nanomaterials produced by green synthesis approaches can offer additional benefits, including reduced energy inputs and lower production costs than traditional synthesis, which bodes well for commercial-scale production. The biomolecules and phytochemicals extracted from microbes and plants, respectively, are active compounds that function as reducing and stabilizing agents for the green synthesis of nanoparticles. Microorganisms, such as bacteria, yeasts, fungi, and algae, have been used in nanomaterials' biological synthesis for some time. Furthermore, the use of plants or plant extracts for metal and metal-based hybrid nanoparticle synthesis represents a novel green synthesis approach that has attracted significant research interest. This review discusses various biosynthesis approaches via microbes and plants for the green preparation of metal and metal oxide nanoparticles and provides insights into the molecular aspects of the synthesis mechanisms and biomedical applications. The use of agriculture waste as a potential bioresource for nanoparticle synthesis and biomedical applications of biosynthesized nanoparticles is also discussed.

Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic Macrophomina phaseolina

Efficacy of a β-1,4-glucosidase from Trichoderma harzianum T12 (ThBglT12) in disrupting the cell wall of the phytopathogenic fungus M. phaseolina (Macrophomina phaseolina) was studied, as the underlying molecular mechanisms of cell wall recognition remains elusive. In this study, the binding location identified by a consensus of residues predicted by COACH tool, blind docking, and multiple sequence alignment revealed that molecular recognition by ThBglT12 occurred through interactions between the α-1,3-glucan, β-1,3-glucan, β-1,3/1,4-glucan, and chitin components of M. phaseolina, with corresponding binding energies of -7.4, -7.6, -7.5 and -7.8 kcal/mol. The residue consensus verified the participation of Glu172, Tyr304, Trp345, Glu373, Glu430, and Trp431 in the active site pocket of ThBglT12 to bind the ligands, of which Trp345 was the common interacting residue. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), total energy, and minimum distance calculation from molecular dynamics (MD) simulation further confirmed the stability and the closeness of the binding ligands into the ThBglT12 active site pocket. The h-bond occupancy by Glu373 and Trp431 instated the role of the nucleophile for substrate recognition and specificity, crucial for cleaving the β-1,4 linkage. Further investigation showed that the proximity of Glu373 to the anomeric carbon of β-1,3/1,4-glucan (3.5 Å) and chitin (5.5 Å) indicates the nucleophiles' readiness to form enzyme-substrate intermediates. Plus, the neighboring water molecule appeared to be correctly positioned and oriented towards the anomeric carbon to hydrolyze the β-1,3/1,4-glucan and chitin, in less than 4.0 Å. In a nutshell, the study verified that the ThBglT12 is a good alternative fungicide to inhibit the growth of M. phaseolina.Communicated by Ramaswamy H. Sarma.

ALD based nanostructured zinc oxide coated antiviral silk fabric

The COVID-19 pandemic has underscored the importance of research and development in maintaining public health. Facing unprecedented challenges, the scientific community developed antiviral drugs, virucides, and vaccines to combat the infection within the past two years. However, an ever-increasing list of highly infectious SARS-CoV-2 variants (gamma, delta, omicron, and now ba.2 stealth) has exacerbated the problem: again raising the issues of infection prevention strategies and the efficacy of personal protective equipment (PPE). Against this backdrop, we report an antimicrobial fabric for PPE applications. We have fabricated a nanofibrous silk-PEO material using electrospinning followed by zinc oxide thin film deposition by employing the atomic layer deposition technique. The composite fabric has shown 85% more antibacterial activity than the control fabric and was found to possess substantial superoxide dismutase–mimetic activity. The composite was further subjected to antiviral testing using two different respiratory tract viruses: coronavirus (OC43: enveloped) and rhinovirus (RV14: non-enveloped). We report a 95% reduction in infectious virus for both OC43 and RV14 from an initial load of ∼1 × 10⁵ (sample size: 6 mm dia. disk), after 1 h of white light illumination. Furthermore, with 2 h of illumination, ∼99% reduction in viral infectivity was observed for RV14. High activity in a relatively small area of fabric (3.5 × 10³ viral units per mm²) makes this antiviral fabric ideal for application in masks/PPE, with an enhanced ability to prevent antimicrobial infection overall.

This study presents an antiviral self-cleaning fabric for masks/PPE applications with protection against human coronavirus.

Green approaches for the synthesis of metal and metal oxide nanoparticles using microbial and plant extracts

Green synthesis approaches are gaining significance as promising routes for the sustainable preparation of nanoparticles, offering reduced toxicity towards living organisms and the environment.

Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis

The development of artificial biocrust using cyanobacterium Phormidium tenue has been suggested as an effective strategy to prevent soil degradation. Here, a combination of in silico approaches with growth rate, photosynthetic pigment, morphology, and transcript analysis was used to identify specific genes and their protein products in response to 500 mM NaCl in P. tenue. The results show that 500 mM NaCl induces the expression of genes encoding glycerol-3-phosphate dehydrogenase (glpD) as a Flavoprotein, ribosomal protein S12 methylthiotransferase (rimO), and a hypothetical protein (sll0939). The constructed co-expression network revealed a group of abiotic stress-responsive genes. Using the Basic Local Alignment Search Tool (BLAST), the homologous proteins of rimO, glpD, and sll0939 were identified in the P. tenue genome. Encoded proteins of glpD, rimO, and DUF1622 genes, respectively, contain (DAO and DAO C), (UPF0004, Radical SAM and TRAM 2), and (DUF1622) domains. The predicted ligand included 22B and MG for DUF1622, FS5 for rimO, and FAD for glpD protein. There was no direct disruption in ligand-binding sites of these proteins by Na+, Cl-, or NaCl. The growth rate, photosynthetic pigment, and morphology of P. tenue were investigated, and the result showed an acceptable tolerance rate of this microorganism under salt stress. The quantitative real-time polymerase chain reaction (qRT-PCR) results revealed the up-regulation of glpD, rimO, and DUF1622 genes under salt stress. This is the first report on computational and experimental analyses of the glpD, rimO, and DUF1622 genes in P. tenue under salt stress to the best of our knowledge.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03050-w.